thanks for all the replies..
especially g1smd.. I think you understood my question the best..
I have started to slowly (but carefully) redirect all those 700 URLS without touching the homepage.. I don't care about the traffic from those 700 pages as long as I retain the traffic my index page gets at the olddomain.com
what I understood from g1smd's post is that as long as I don't (by mistake) redirect the root, and the new URLs that will appear on the olddomain.com, I will be fine..
that's all I needed to know..